Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes

Patel et al., 2023

homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Freyman et al., 2023

Exploring evolutionary adaptations of leaf heteroblasty in subspecific taxa of Hawaiian Chenopodium oahuense

Bullock and Cantley, 2022

Including Phylogenetic Conservatism of Shortgrass Prairie Restoration Desired Species Does Not Improve Species Germination Predictions

Chen et al. 2022

Landscapes of Linalool

Are Palmer’s Elm-Leaf Goldenrod and the Smooth Elm-Leaf Goldenrod Real? The Angiosperms353 Kit Provides Within-Species Signal in Solidago ulmifolia s. l.

Beck et al., 2021

On the Potential for Angiosperms353 for Population Genomics

Slimp et al. 2020

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

Hale et al. 2020

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Liu, Johnson et al. 2019. Nat. Comm.

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering

Johnson et al. 2018. SystBio.

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

Kates et al. 2018. APPS.

Practical considerations for plant phylogenomics

McKain et al. 2018. MPE.

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

Medina et al. 2018. MPE.

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High- Throughput Sequencing Reads Using Target Enrichment

Johnson et al. 2016. APPS.

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

Devos et al. 2016. New Phyt.

A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta)

Johnson et al. 2016. MPE.

Evidence for genetic erosion of a California native tree, Platanus racemosa, via recent, ongoing introgressive hybridization with an introduced ornamental species

Johnson et al. 2016 Con. Gen.

Evolution of niche preference in Sphagnum peat mosses

Johnson et al. 2014 Evolution